The game contains very similar gameplay to the previous games, with the similar 'point and click' approach. However, it has hardly any hotkeys as compared to the previous installment, and the user has to use buttons at the bottom of the screen on the action bar.

As in Commandos 1 and 2, you are able to see all enemies on the map, follow their movements, and make attacks depending on their behavior. There are a few differences, such as the addition of an 'Assault Rifle' - a weapon less powerful than a rifle, but more powerful than a pistol. Also, all units are able to use weapons such as the grenade, rather than just the Sapper as in previous games. The previous "knapsack" setup simply showing a picture of all the items the currently selected commando has in his possesion superimposed over a picture of a rucsac has been abandoned in favor of a "box".

When the inventory is selected, there are multiple blocks to put items in, such as grenades (1 block), pistols (1 block), rifles (4 blocks horizontal), enemy uniforms (4 blocks square), submachineguns (4 blocks square) and timebombs (2 blocks horizontal). When searching enemies bodies or supply crates, a similar, but smaller box is shown for their capacity. Commandos such as the Green Beret or Spy, who in earlier games have only been armed with the regulation pistol, can now use almost all the small arms available, except for the sniper rifle.

While adding realism (the Commandos are no longer useless outside their area of expertise), some players complain this robs the Commandos of their individual roles within the group, making them more general. This does however, make the missions less linear, owing to the fact that the same job can done by different Commandos.

The new "cover mode" ability allows the player to leave Commandos waiting at a door or behind cover, ready to shoot at any enemy that comes within range, often with more accuracy than when controlled manually. This gives the option of ambushes, and more defensive tactics.

Instead of the previous, long, single campaign, this game is broken down into 3 campaigns: Central Europe, Normandy and Stalingrad; each containing a various amount of missions, some shorter than others.

However, the game has been criticized for being difficult to play on account of having fewer hotkeys than its predecessors. The player has to control the commandos using the buttons in the pop-up menu at the bottom of the screen. Also, the game is locked at a 800x600 resolution which is low by today's standards.